Henneguya cuniculator sp. nov. was found infecting spotted sorubim catfish Pseudoplatystoma corruscans from the São Francisco River, Minas Gerais, Brazil. The parasites form elongated plasmodia of up to 1 cm in length in the gill filaments. Mature spores were ellipsoidal from the frontal view, with total length of 29.4 ±2.4 (mean ±SD, range 23.3-32.4) μm, body length of 12.1 ±1.0 (10.0-14.7) μm, width of 4.8 ±0.4 (4.0-5.9) μm, and tail length of 16.7 ±2.0 (12.3-19.4) μm. From the lateral view, spores were biconvex, with thickness of 4.2 ±0.7 (3.9-4.9) μm. The polar capsules were elongated and equal in size, 6.2 ±0.3 (5.2-6.2) μm in length, and 1.8 ±0.1 (1.4-1.9) μm in width. Ultrastructural analysis showed that the plasmodial wall had delicate projections towards the host tissue and a thin layer that prevented contact between the host cells and the parasite. 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